Align Serine transporter (characterized)
to candidate 16926 b2845 predicted transporter (NCBI)
Query= SwissProt::P0AAD6 (429 letters) >FitnessBrowser__Keio:16926 Length = 409 Score = 305 bits (781), Expect = 2e-87 Identities = 161/415 (38%), Positives = 265/415 (63%), Gaps = 16/415 (3%) Query: 18 WRKTDTMWMLGLYGTAIGAGVLFLPINAGVGGMIPLIIMAILAFPMTFFAHRGLTRFVLS 77 W K +T+W LYGTA+GAG LFLPI G G + L I A++A+P+T++ H+ L +F+LS Sbjct: 5 WSKEETLWSFALYGTAVGAGTLFLPIQLGSAGAVVLFITALVAWPLTYWPHKALCQFILS 64 Query: 78 GK-NPGEDITEVVEEHFGIGAGKLITLLYFFAIYPILLVYSVAITNTVESFMSHQLGMTP 136 K + GE IT V ++G G LIT LYF A + ++L+Y+VAITN++ ++ + + Sbjct: 65 SKTSAGEGITGAVTHYYGKKIGNLITTLYFIAFFVVVLIYAVAITNSLTEQLAKHMVIDL 124 Query: 137 PPRAILSLILIVGMMTIVRFGEQMIVKAMSILVFPFVGVLMLLALYLIPQWNGAALETLS 196 R ++SL +++ + I G ++ M LVFP + + L++YL+ W L T Sbjct: 125 RIRMLVSLGVVLILNLIFLMGRHATIRVMGFLVFPLIAYFLFLSIYLVGSWQPDLLTT-- 182 Query: 197 LDTASATGNGLWMTLWLAIPVMVFSFNHSPIISSFAVAKREEYGDMAEQKCSKILAFAHI 256 N L +W++IPVMVF+F+H+PIIS+FA+ +RE+YG+ A KC KI+ A++ Sbjct: 183 --QVEFNQNTLHQ-IWISIPVMVFAFSHTPIISTFAIDRREKYGEHAMDKCKKIMKVAYL 239 Query: 257 MMVLTVMFFVFSCVLSLTPADLAAAKEQNISILSYLANHFNAPVIAWMA---PIIAIIAI 313 ++ ++V+FFVFSC+LS+ P+ + AAKE+ ++ILS L+ NAP AW++ I+A++A+ Sbjct: 240 IICISVLFFVFSCLLSIPPSYIEAAKEEGVTILSALSMLPNAP--AWLSISGIIVAVVAM 297 Query: 314 TKSFLGHYLGAREGFNGMVIKSLR--GKGKSIEINKLNRITALFMLVTTWIVATLNPSIL 371 +KSFLG Y G EG +V +L+ G KS N+ ++ + + + T+IV +NP+ + Sbjct: 298 SKSFLGTYFGVIEGATEVVKTTLQQVGVKKSRAFNR--ALSIMLVSLITFIVCCINPNAI 355 Query: 372 GMIETLGGPIIAMILFLMPMYAIQKVPAMRKYSGHISNVFVVVMGLIAISAIFYS 426 MI + GP+IAMILF+MP + +PA++ + I N+ +++G++ +S +F+S Sbjct: 356 SMIYAISGPLIAMILFIMPTLSTYLIPALKPWRS-IGNLITLIVGILCVSVMFFS 409 Lambda K H 0.328 0.140 0.416 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 498 Number of extensions: 21 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 429 Length of database: 409 Length adjustment: 32 Effective length of query: 397 Effective length of database: 377 Effective search space: 149669 Effective search space used: 149669 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory